Origin IGS: gtcctgttcttttttaatgaggtcatcgtcatgttttattcttacagagaaggagaggaataattattcatgtaaaaacaaaaaacatgtgcaacttcctcccctacctatgaagtacctgacaaaggtacgataaaataaagaaattccaattcatccgacaaggacggatcgctcctttttcagccctatcaccttatcccaactttcgatccatccta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taggatggatcgaaagttgggataaggtgatagggctgaaaaaggagcgatccgtccttgtcggatgaattggaatttctttattttatcgtacctttgtcaggtacttcataggtaggggaggaagttgcacatgttttttgtttttacatgaataattattcctctccttctctgtaagaataaaacatgacgatgacctcattaaaaaagaacaggac Mask Tandem Repeat Region ================================================ gtcctgttcttttttaatgaggtcatcgtcatgttttattcttacagagaaggagaggaataattattcatgtaaaaacaaaaaacatgtgcaacttcctcccctacctatgaagtacctgacaaaggtacgataaaataaagaaattccaattcatccgacaaggacggatcgctcctttttcagccctatcaccttatcccaactttcgatccatccta Find is-nt database================================================ Query_seq: TF2458:TF2459|TF2458:TF2459:ribosome-binding factor A:conserved hypothetical protein:->->:2635706..2635926 221 gtcctgttcttttttaatgaggtcatcgtcatgttttattcttacagagaaggagaggaataattattcatgtaaaaacaaaaaacatgtgcaacttcctcccctacctatgaagtacctgacaaaggtacgataaaataaagaaattccaattcatccgacaaggacggatcgctcctttttcagccctatcaccttatcccaactttcgatccatccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2458:TF2459|TF2458:TF2459:ribosome-binding factor A:conserved hypothetical protein:->->:2635706..2635926 221 gtcctgttcttttttaatgaggtcatcgtcatgttttattcttacagagaaggagaggaataattattcatgtaaaaacaaaaaacatgtgcaacttcctcccctacctatgaagtacctgacaaaggtacgataaaataaagaaattccaattcatccgacaaggacggatcgctcctttttcagccctatcaccttatcccaactttcgatccatccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2458:TF2459|TF2458:TF2459:ribosome-binding factor A:conserved hypothetical protein:->->:2635706..2635926 221 gtcctgttcttttttaatgaggtcatcgtcatgttttattcttacagagaaggagaggaataattattcatgtaaaaacaaaaaacatgtgcaacttcctcccctacctatgaagtacctgacaaaggtacgataaaataaagaaattccaattcatccgacaaggacggatcgctcctttttcagccctatcaccttatcccaactttcgatccatccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtcctgttcttttttaatgaggtcatcgtcatgttttattcttacagagaaggagaggaataattattcatgtaaaaacaaaaaacatgtgcaacttcctcccctacctatgaagtacctgacaaaggtacgataaaataaagaaattccaattcatccgacaaggacggatcgctcctttttcagccctatcaccttatcccaactttcgatccatccta Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 17 End: 133 ................ M R S S S C F I L T E K E R N N Y S C K N K K H V Q L P P L P M K Y L T K V R ........................................................................................ gtcctgttcttttttaatgaggtcatcgtcatgttttattcttacagagaaggagaggaataattattcatgtaaaaacaaaaaacatgtgcaacttcctcccctacctatgaagtacctgacaaaggtacgataaaataaagaaattccaattcatccgacaaggacggatcgctcctttttcagccctatcaccttatcccaactttcgatccatccta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtcctgttcttttttaatgaggtcatcgtcatgttttattcttacagagaaggagaggaataattattcatgtaaaaacaaaaaacatgtgcaacttcctcccctacctatgaagtacctgacaaaggtacgataaaataaagaaattccaattcatccgacaaggacggatcgctcctttttcagccctatcaccttatcccaactttcgatccatccta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2458:TF2459|TF2458:TF2459:ribosome-binding factor A:conserved hypothetical protein:->->:2635706..2635926 221 gtcctgttcttttttaatgaggtcatcgtcatgttttattcttacagagaaggagaggaataattattcatgtaaaaacaaaaaacatgtgcaacttcctcccctacctatgaagtacctgacaaaggtacgataaaataaagaaattccaattcatccgacaaggacggatcgctcctttttcagccctatcaccttatcccaactttcgatccatccta Intra-Species Hit: Count: 1 Min: 1 Max: 221 Len: 221 Subject: tfor_TF2458_TF2459|ribosome-binding factor A:conserved hypothetical protein|POSITIVE:POSITIVE|[2635706,2635926]|221 HSP 1 e-value: 1.0E-100 bit: 367.0 Len: 221 Query Start:1 Query End:221 Subject Strand: POSITIVE Subject Start: 1 Subject End: 221 gtcctgttcttttttaatgaggtcatcgtcatgttttattcttacagagaaggagaggaataattattcatgtnnnnnnnnnnnncatgtgcaacttcctcccctacctatgaagtacctgacaaaggtacgataaaataaagaaattccaattcatccgacaaggacggatcgctcctttttcagccctatcaccttatcccaactttcgatccatccta gtcctgttcttttttaatgaggtcatcgtcatgttttattcttacagagaaggagaggaataattattcatgtaaaaacaaaaaacatgtgcaacttcctcccctacctatgaagtacctgacaaaggtacgataaaataaagaaattccaattcatccgacaaggacggatcgctcctttttcagccctatcaccttatcccaactttcgatccatccta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCCUGUUCUUUUUUAAUGAGGUCAUCGUCAUGUUUUAUUCUUACAGAGAAGGAGAGGAAUAAUUAUUCAUGUAAAAACAAAAAACAUGUGCAACUUCCUCCCCUACCUAUGAAGUACCUGACAAAGGUACGAUAAAAUAAAGAAAUUCCAAUUCAUCCGACAAGGACGGAUCGCUCCUUUUUCAGCCCUAUCACCUUAUCCCAACUUUCGAUCCAUCCUA (((.............((((.(....).))))......(((((..((.(.(((.((((((........(((((...........)))))......)))))).))).))).....((((((.....)))))).........)))))..............))).((((.((((((...................................)))))).)))). (-43.29) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGAUGGAUCGAAAGUUGGGAUAAGGUGAUAGGGCUGAAAAAGGAGCGAUCCGUCCUUGUCGGAUGAAUUGGAAUUUCUUUAUUUUAUCGUACCUUUGUCAGGUACUUCAUAGGUAGGGGAGGAAGUUGCACAUGUUUUUUGUUUUUACAUGAAUAAUUAUUCCUCUCCUUCUCUGUAAGAAUAAAACAUGACGAUGACCUCAUUAAAAAAGAACAGGAC .(((((((((((.............(((......)))..........))))))))))).....(((((((((..((...((((((((...((((((.....))))))...(((((.((((((((((((((..(((((...........)))))..))))..)))))))))).).)))).))))))))..))..))))....)))))............... (-55.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 391 196 157 52 2 tfor:TF2898|5end_conserved_hypothetical_protein_3087061..3087291_POSITIVE 364 219 174 191 145 tfor:TF3096|5end_conserved_hypothetical_protein_3327963..3328193_POSITIVE 333 190 151 142 105 tfor:TF2348|5end_outer_membrane_protein,_possibly_involved_in_nutrient_binding_2511088..2511318_POSITIVE 327 189 149 129 88 tfor:TF2231|5end_DNA_methylase,_site-specific_DNA-methyltransferase_(adenine-specific)_2400307..2400537_POSITIVE 327 188 141 57 13 tfor:TF1543|5end_conserved_hypothetical_protein_1649429..1649659_POSITIVE 326 206 164 175 131 tfor:TF1755|5end_periplasmic_protease_1891774..1892004_POSITIVE 321 178 146 81 46 tfor:TF0240|5end_conserved_hypothetical_protein;_possible_gycosyltransferase_I_family_protein_270086..270316_POSITIVE 317 193 157 172 125 tfor:TF2248|5end_transfer_region-related_protein,_TraB_2422551..2422781_POSITIVE 316 185 147 199 151 tfor:TF1758|5end_conserved_hypothetical_protein_1894769..1894999_POSITIVE 314 199 158 43 1 tfor:TF2547|5end_hypothetical_protein_2730664..2730894_POSITIVE 314 196 157 191 151 tfor:TF0678|5end_hypothetical_protein_721103..721333_POSITIVE 312 199 157 182 130 tfor:TF0816|5end_hypothetical_protein_874217..874447_POSITIVE 308 188 156 80 42 tfor:TF2793|5end_possible_L-lysine_2,3-aminomutase_2977661..2977891_POSITIVE 308 196 157 205 165 tfor:TF0822|5end_hypothetical_protein_880487..880717_POSITIVE 308 196 157 205 165 tfor:TF0821|5end_hypothetical_protein_879879..880109_POSITIVE 304 198 153 176 130 tfor:TF0086|5end_ABC_transporter,_ATP-binding_protein_92434..92664_POSITIVE 302 200 156 128 75 tfor:TF2824|5end_nucleoside-transporting_protein_nupG_3014701..3014931_POSITIVE 301 190 146 98 45 tfor:TF0296|5end_hypothetical_protein_321941..322171_POSITIVE 299 190 149 73 30 tfor:TF1516|5end_transposase_fragment_1626407..1626637_POSITIVE 299 215 171 72 37 tfor:TF1240|5end_conserved_hypothetical_protein_1324304..1324534_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 333 190 151 66 29 tfor:TF2347|3end_outer_membrane_protein,_TonB_dependent_receptor_2511092..2511242_POSITIVE 327 189 149 136 95 tfor:TF2230|3end_CTn_excision_protein_2400394..2400544_POSITIVE 327 188 141 50 6 tfor:TF1542|3end_transcriptional_regulator_1649502..1649652_POSITIVE 318 187 158 87 53 tfor:TF1815|3end_conserved_hypothetical_protein_1957442..1957592_POSITIVE 315 187 157 151 119 tfor:TF2247|3end_transfer_region-related_protein,_TraA_2422625..2422775_POSITIVE 298 200 155 48 1 tfor:TF2614|3end_conserved_hypothetical_protein_2790636..2790786_POSITIVE 296 214 176 145 100 tfor:TF1489|3end_argininosuccinate_lyase_1590318..1590468_POSITIVE 296 201 165 129 73 tfor:TF0308|3end_hypothetical_protein_334082..334232_POSITIVE 293 200 151 83 31 tfor:TF0263|3end_ISPg3_(IS195)_transposase_292654..292804_POSITIVE 292 188 147 83 40 tfor:TF1326|3end_hypothetical_protein_1404100..1404250_POSITIVE 291 128 95 52 12 tfor:TF2687|3end_iron-regulated_ABC-type_transporter_membrane_component_2864962..2865112_POSITIVE 288 190 145 136 85 tfor:TF1274|3end_hypothetical_protein_1357895..1358045_POSITIVE 281 189 148 51 7 tfor:TF0169|3end_possible_CRISPR-associated_protein_Cas1_179643..179793_POSITIVE 278 212 172 59 11 tfor:TF2225|3end_CTn_excision_protein_2395602..2395752_POSITIVE 277 188 160 70 42 tfor:TF2657|3end_conserved_hypothetical_protein_2830873..2831023_POSITIVE 273 150 107 80 35 tfor:TF2290|3end_ABC_transporter,_ATP-binding/permease_component_2446178..2446328_POSITIVE 272 196 158 90 54 tfor:TF2749|3end_possible_hemolysin_2934518..2934668_POSITIVE 268 128 83 86 31 tfor:TF3087|3end_conserved_hypothetical_protein_3322582..3322732_POSITIVE 265 188 150 107 63 tfor:TF2924|3end_DNA-binding_response_regulator/sensor_histidine_kinase_3125618..3125768_POSITIVE 264 200 157 91 43 tfor:TF3165|3end_thiol:disulfide_interchange_protein,_thioredoxin_family_protein_3405343..3405493_POSITIVE